June 2015 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Galaxy admin access
by Dannon Baker 23 Jun '15

23 Jun '15

In your terminal, you'll need to navigate to the galaxy config directory (you'll see the .sample file there) first. Once there, look at a directory list and make sure that an existing galaxy.ini isn't already there. Also, please keep the galaxy-dev list cc'd instead of replying directly so that others might be able to help you as well. On Wed, Jun 17, 2015 at 12:18 PM Davenport, Aneisha <ADAVENP3(a)gru.edu> wrote: > I'm typing the command in terminal > > > -------- Original message -------- > From: Dannon Baker <dannon.baker(a)gmail.com> > Date: 06/17/2015 12:05 PM (GMT-05:00) > To: "Davenport, Aneisha" <ADAVENP3(a)gru.edu>, > galaxy-dev(a)lists.galaxyproject.org > Subject: Re: [galaxy-dev] Galaxy admin access > > Where are you executing this? You'll need to be in the galaxy/config > directory, where galaxy.ini.sample exists. > > I'm looping the mailing list back in on this so other people might also be > able to help. > > On Wed, Jun 17, 2015 at 8:28 AM Davenport, Aneisha <ADAVENP3(a)gru.edu> > wrote: > >> When I type in cp galaxy.ini.sample galaxy.ini in terminal it outputs no >> such file or directory >> >> >> -------- Original message -------- >> From: Dannon Baker <dannon.baker(a)gmail.com> >> Date: 06/15/2015 3:14 PM (GMT-05:00) >> To: "Davenport, Aneisha" <ADAVENP3(a)gru.edu> >> Subject: Re: [galaxy-dev] Galaxy admin access >> >> I'm not sure what you mean. You can edit the file using any text >> editor, try 'nano', or emacs or vim if you're more comfortable with those. >> >> Does the file exist or not? If not, simply "cp galaxy.ini.sample >> galaxy.ini" will do it. >> >> On Mon, Jun 15, 2015 at 7:27 AM Davenport, Aneisha <ADAVENP3(a)gru.edu> >> wrote: >> >>> How do I create it and edit it on terminal? >>> >>> Aneisha Davenport >>> ________________________________________ >>> From: Dannon Baker [dannon.baker(a)gmail.com] >>> Sent: Friday, June 12, 2015 9:44 PM >>> To: Davenport, Aneisha; galaxy-dev(a)lists.galaxyproject.org >>> Subject: Re: [galaxy-dev] Galaxy admin access >>> >>> Hi Aneisha, >>> >>> When you say you cannot alter config/galaxy.ini, what do you mean? You >>> should be able to create (if not there) and edit this file in your regular >>> terminal on that machine. >>> >>> Does a different user own the file, perhaps a 'galaxy' one? If so, you >>> could change to that user and then edit. >>> >>> On Fri, Jun 12, 2015 at 5:13 PM Davenport, Aneisha <ADAVENP3(a)gru.edu >>> <mailto:ADAVENP3@gru.edu>> wrote: >>> Hi, I work at the It service desk at the GRU Health and Science campus >>> Ed Commons GB building and I have a customer trying to get admin access for >>> the local installation of galaxy. We tried to follow the online >>> instructions "In order to control your new Galaxy through the UI >>> (installing tools, managing users, creating groups etc.) you have to become >>> an administrator. First register as a new user and then give the user admin >>> privileges like this: You add the Galaxy login ( email ) to the Galaxy >>> configuration file (config/galaxy.ini). If the file does not exist you can >>> copy it from the provided sample (config/galaxy.ini.sample). Note that you >>> have to restart Galaxy after modifying the configuration for changes to >>> take effect. >>> >>> >>> # this should be a comma-separated list of valid Galaxy users >>> admin_users = user1(a)example.com<mailto:user1@example.com>, >>> user2(a)example.com<mailto:user2@example.com>" but we cannot alter the >>> config/galaxy.ini file. Can you please give us assistance? Do you run in >>> console or Terminal (this is a Macbook Air Laptop)? >>> >>> >>> Aneisha Davenport >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> https://lists.galaxyproject.org/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> http://galaxyproject.org/search/mailinglists/ >>> >>

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Strange repository dependency behavior with toolshed-installed naive_variant_caller
by Brian Claywell 19 Jun '15

19 Jun '15

First, I'm at a bit of a loss to even describe what's going on, so I apologize in advance for a rambling bug report. Please bear with me! The naive_variant_caller tool was failing on our instance with "Failed to resolve dependency" errors on numpy, pyBamParser, and pyBamTools, despite the tool dependencies and their respective dependency packages being installed. I attempted to use the "repair repository" action on naive_variant_caller with no success. I then uninstalled naive_variant_caller, package_numpy_1_7, package_pybamparser_0_0_1, and package_pybamtools_0_0_1 and attempted to reinstall naive_variant_caller from scratch, again allowing Galaxy to manage the dependencies. This time, the dependencies resolved (at least as far as the "Building dependency shell command" messages were concerned), but naive_variant_caller still failed, this time with an import error: ImportError: No module named pyBamTools.genotyping.naive Digging around a little I found that the env.sh that was sourced for pyBamTools was looking for an env.sh in another pyBamTools revision directory, but the revision it was looking for didn't exist. Then I looked in the admin interface and saw that package_pybamtools_0_0_1 and package_pybamparser_0_0_1 were each installed twice; each had both the most recent revision and an older revision with the "updates are available" icon. At this point I uninstalled naive_variant_caller and all of its dependency packages again. I then installed naive_variant_caller from the toolshed *without* dependency management, and manually installed the required revisions of numpy, pybamparser, and pybamtools. Finally naive_variant_caller started working. However, naive_variant_caller is now shown in the admin interface as "Installed, missing repository dependencies", and the installed repository page shows that the dependencies are a very strange state (see attached screenshot). That is, the same revision of numpy is listed as installed twice, and the pybamparser and pybamtools dependencies are each listed as simultaneously installed and uninstalled. Can anyone shed some light on what could be happening and what to do about it? Is there some external way to verify the consistency of a tool and its dependencies? Thanks! Cheers, Brian -- Brian Claywell | programmer/analyst Matsen Group | http://matsen.fredhutch.org <http://matsen.fhcrc.org/> Fred Hutchinson Cancer Research Center

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cheetah chaet sheet
by Alexander Vowinkel 19 Jun '15

19 Jun '15

Hi, someone knows a cheat sheet with all the commands supported by cheetah? Best, Alexander

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Custom Tool Dev Questions
by Ryan G 19 Jun '15

19 Jun '15

Hi all - I have a tool which is essentially an entire NGS pipeline bundled into a perl script and associated modules. I'd like to offer this tool to users via Galaxy. I'm trying to pass a bunch of fastq files to the tool, but noticed that operating on multiple datasets creates a separate job for each dataset. I want to pass all the datasets to the tool so only one galaxy job is actually created. Is this possible, and if so, how do I go about doing this? Ryan

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BAM datatype - bam & bai
by Alexander Vowinkel 19 Jun '15

19 Jun '15

Hi, when I 'produce' a bam file in my output, I can download the bam file and a corresponding bai file. I am now wondering where does the bai file come from? When is it being generated, what code is used for that? When I do multiple actions with my bam file - is the index generated every time? (overhead) Where is the bai saved on disk (if it is)? I found that in the IUC gatk, a new bai is always generated when a gatk tool is started. This creates quite an overhead. Isn't there a better solution? @ref https://github.com/galaxyproject/tools-iuc/issues/194 Best, Alexander

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macro tag naming conventions
by Alexander Vowinkel 19 Jun '15

19 Jun '15

Hi, in https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#Direct_XML_Macr…, macros are defined with <macro name="dbKeyActions"> [...] </macro> But when I look in IUC macros, I find the following: <xml name="..."> [...] </xml> Which one is the current standard? Best, Alexander

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package_bowtie_2_2_4 Executable Permissions - can't run bowtie as non-galaxy user
by David Trudgian 19 Jun '15

19 Jun '15

Installed bowtie2 from the toolshed, which brings in package_bowtie_2_2_4, which downloads bowtie binaries from depot.galaxyproject.org http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.2.4-l… Jobs submitted on our setup, running as a 'real user' (not galaxy user) via pulsar + SLURM fail with a permissions error. This is due to the permissions on some of the bowtie executables in the .tar.gz from depot being owner/group executable only. Other users cannot run bowtie2: -rwxrwx---. 1 galaxy galaxy 18K Oct 22 2014 bowtie2 If I download the tar.gz from depot manually and extract then I get: -rwxrwx--- 1 dtrudgian biohpc_admin 18K Oct 22 2014 bowtie2 Could the .tar.gz be fixed, so that the executables will work in a run as real user configuration? Is there any sensible way Galaxy could enforce permissions to guard against this issue? Cheers, -- David Trudgian Ph.D. Computational Scientist, BioHPC UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 Please contact biohpc-help@utsouthwestern with general BioHPC inquries. ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Bug in commit 38679a0
by Ryan G 18 Jun '15

18 Jun '15

In scripts/functional_tests.py, line 71, the change is causing a directory called "test-data,https://github.com/galaxyproject/galaxy- test-data.git" to get created. I'm not sure that's the intention of this fix. default_galaxy_test_file_dir is assigned to test_dir, then never used again. test_dir is used to create the testing directory.

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table_recalibration cannot be installed through tool_shed
by Jingchao Zhang 18 Jun '15

18 Jun '15

Hi all, The table_recalibration tool cannot be installed through tool_shed. There seems to be a broken link for the repository. (https://toolshed.g2.bx.psu.edu/repos/devteam/table_recalibration/gatk_table…) Here is the most recent log from the "Automated tool test results" 2015-05-07 10:37:18 Automated test environment Time tested: 2015-05-07 10:37:18 System: Linux 3.13.0-36-generic Architecture: x86_64 Python version: 2.7.6 Galaxy revision: v15.03.2-904-g3e80076 Galaxy database version: 128 Tool shed revision: 16935:64266df71fa7 Tool shed database version: 25 Tool shed mercurial version: 3.2.4 Installation errors This repository Error Error getting revision 30e1dd77e99c of repository table_recalibration owned by devteam: An entry for the repository was not found in the database. Can someone please help to fix this? Thanks, Jingchao

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Fwd: Adding packages for bedtools and ucsc-utils for Trackster?
by Eric Rasche 18 Jun '15

18 Jun '15

(We discussed this over IRC, but responding to the list posting for posterity/searchability) The JSON.pm file isn't found in your PERL5LIB path because the original version of my JBrowse tool failed to specify the full dependency list and assumed you had some perl modules manually installed. The latest version of my JBrowse tool now includes the full set of dependencies. Since chatting on IRC, this version has been uploaded to the MTS and is available here: https://toolshed.g2.bx.psu.edu/view/iuc/jbrowse/497c6bb3b717 (For the rest of the mailing list reading this, an unofficial release announcement) JBrowse 1.11.6 is available as a tool which can be run and can display: - bed/gff/gff3 - BAM - Blast XML data (automatically converted to gapped GFF3 and displayed with evalue-based intensities) - BigWig data - VCF data putting it closer to being on-par with trackster. It's an excellent end-of-workflow step to summarize all of your generated genomic analyses. If any of the community have feature requests, send them my way! NB: BAM/BigWigs do NOT play nicely with galaxy if you aren't using X-SendFile. 2015-06-18 5:42 GMT-05:00 Peter van Heusden <pvh(a)sanbi.ac.za>: > Thanks Bjoern > > My initial install didn't pick up the Perl dependencies correctly, but I > re-installed and now the install seems to have the required modules but is > missing something in the environment variables. Specifically I get an error > import JSON.pm, see below. Note that the > jbrowse/1.11.6/iuc/package_jbrowse_1_11_6/d5ab749c9e97/lib/perl5 directory > isn't included in @INC and in fact the paths that *are* included seem to > imply that the wrong perl interpreter is being picked up. > > > Fatal error: Exit code 1 () > Can't locate JSON.pm in @INC (you may need to install the JSON module) (@INC contains: /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/JSON.pm line 10. > BEGIN failed--compilation aborted at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/JSON.pm line 10. > Compilation failed in require at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 21. > BEGIN failed--compilation aborted at /net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/job_working_directory/000/29/dataset_29_files/JBrowse-1.11.6/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 21. > Compilation failed in require at bin/prepare-refseqs.pl line 7. > BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 7. > Traceback (most recent call last): > File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/2c9e5136b416/jbrowse/jbrowse.py", line 44, in <module> > process_genome(jbrowse_dir, os.path.realpath(args.genome.name)) > File "/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/2c9e5136b416/jbrowse/jbrowse.py", line 17, in process_genome > subprocess.check_output(['perl', 'bin/prepare-refseqs.pl', '--fasta', genome], cwd=jbrowse_dir) > File "/usr/lib/python2.7/subprocess.py", line 573, in check_output > raise CalledProcessError(retcode, cmd, output=output) > subprocess.CalledProcessError: Command '['perl', 'bin/prepare-refseqs.pl', '--fasta', '/net/datasrv3hs.sanbi.ac.za/cip0/software/galaxy/galaxysrv/galaxy/database/files/000/dataset_3.dat']' returned non-zero exit status 2 > > > On 18 June 2015 at 10:01, Bjoern Gruening <bjoern.gruening(a)gmail.com> > wrote: > >> Peter, >> >> I'm in a hurry ... have a look at >> https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse >> Developed by IUC member Eric Rasche. >> >> Cheers, >> Bjoern >> >> >> On 18.06.2015 10:00, Peter van Heusden wrote: >> >> I've tried that - I've added the Environment Modules for the relevant >> tools to the local_env.sh file, so they're there in the environment when >> Galaxy runs. These tools are scheduled via our cluster, however, so I don't >> think the environment passes across to them. They depend on these Galaxy >> packages, however, and those (bedtools and ucsc-utils) are now installed, >> so I'm not sure why it can't pick them up from the shed_tools. >> >> On 18 June 2015 at 09:10, Hans-Rudolf Hotz <hrh(a)fmi.ch> wrote: >> >>> >>> >>> On 06/18/2015 09:06 AM, Peter van Heusden wrote: >>> >>>> Hi there >>>> >>>> I'm trying to visualise some of our genome data using Trackster. Initial >>>> input is 790,000 lines of GFF3. When I try and create the visualisation, >>>> I get errors from two tools: >>>> >>>> Convert GFF to Interval Index on data 3 >>>> -- an out of memory error - I'll try and fix this by upping the memory >>>> limit for our Galaxy jobs >>>> >>>> Convert BED, GFF, or VCF to BigWig on data 3 >>>> -- bedtools and bedGraphToBigWig not found errors. I tried to resolve >>>> these by installing the ucsc-tools and bedtools packages - and they did >>>> install correctly - but I still get these file not found errors. >>>> >>>> >>> Hi Peter >>> >>> make sure 'galaxy' (ie the user galaxy is running as) has the newly >>> installed tools in its path. You might need to add them to "run.sh" and >>> restart the server. >>> >>> >>> Hans-Rudolf >>> >>> >>> Any idea how to fix this second problem? >>>> >>>> Thanks! >>>> Peter >>>> P.S. as an alternative to Trackster, does anyone have Galaxy interfaced >>>> to JBrowse? >>>> >>>> >>>> ___________________________________________________________ >>>> Please keep all replies on the list by using "reply all" >>>> in your mail client. To manage your subscriptions to this >>>> and other Galaxy lists, please use the interface at: >>>> https://lists.galaxyproject.org/ >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> >>>> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >> >> >> > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru

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